Now is generating my all-classes.js but it is not generated properly.
I think this is related to the structure of my application.

Log from Chrome console:

Code:

Failed to load resource: the server responded with a status of 404 (Not Found)
http://localhost:8080/cbi_extjs_build/proxy/rest.js?_dc=1352111011486
Failed to load resource: the server responded with a status of 404 (Not Found) http://localhost:8080/cbi_extjs_build/Cbi/model/PomiarModel.js?_dc=1352111011509
...

These will then be included in your compiled all-classes.js ahead of app.js. Obviously they will also be loaded after ext-all.js in dev mode as well.

Looking at those paths, however, I am concerned that you may be adding files to the Ext JS framework tree... this is not a safe way to go as framework upgrades can be very problematic as a result. I would highly recommend keeping the Ext JS framework folder unchanged as much as possible and organize your application code outside that folder tree. Perhaps looking at how Sencha Cmd would organize your code may help (even if you cannot reorganize your app, it is a helpful example).

The role of bootstrap is to provide the Loader with path information, similar to Ext.Loader.setPath. What can cause issues with Cmd is making direct calls to Loader to load scripts. This is not something that Cmd can safely remove for you so it does not do so. If you are using this simply to deal with dependencies, then using "requires" and "uses" statements in your class declaration is much better from the perspective of builds.